Yeah the manual trans chances the game. Your dealing with pilot bearing, clutch alignment, etcwhoa....didn't know that! how far back does it push the drivetrain? I'm running my stock driveshaft (had a c200k originally...now an m226).We are also taking into consideration my aftermarket Tom Woods driveshaft. The VK swap pushes the drivetrain back. My driveshaft was measured for the V6 and trans position. This also explains why it will shift fine without the trans. Hopefully I can machine the pinion flange adapter to compensate for the difference.
EDIT - Disregard....my guess is it's pushed back just cause you're dealing with a manual?